SRX11167822
GSM5379224: TF ChIP-seq from SK-N-SH (ENCLB009HGN); Homo sapiens; ChIP-Seq

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CSRNP3

Cell type

Cell type Class
Neural
Cell type
SK-N-SH
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

biosample type
cell line
cell line
SK-N-SH
sex
female
health state
Metastatic neuroblastoma from bone marrow
dev_stage
child
age
4 year
donor ID
ENCDO000ABD
lab
Michael Snyder, Stanford
source
ATCC
treatments
treatment_term_id: CHEBI:15367; treatment_term_name: all-trans-retinoic acid; treatment_type: chemical; duration: 48; duration_units: hour;

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
general protocol: https://www.encodeproject.org/documents/716003cd-3ce7-41ce-b1e3-6f203b6632a0/@@download/attachment/ENCODE4%20_Snyder_ChIP-seq_BiorupterTruSeqProtocol_v1.pdf

Sequencing Platform

instrument_model
Illumina HiSeq 4000

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
41808503
Reads aligned (%)
97.4
Duplicates removed (%)
28.8
Number of peaks
2147 (qval < 1E-05)

hg19

Number of total reads
41808503
Reads aligned (%)
96.6
Duplicates removed (%)
29.1
Number of peaks
1471 (qval < 1E-05)

Base call quality data from DBCLS SRA